BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.

Cactus is a general, modular, parallel environment for solving systems of partial differential
equations. The code has been developed over many years by a large international
collaboration of numerical relativity and computational science research groups and can
be used to provide a portable platform for solving any system of partial differential
equations.

Clarrhmos is a description language and simulator
for myocardial structure and electrophysiology.
Input to the program is a model file specifying
types of cells, action potential shape, refractory
period, 3D placement of the cells, relation of
parameters to other functions, pacing, electrode
placement. Output is a file describing
depolarisation and repolarisation of the
myocardium and electrograms. A graphic tool for
interactive inspection of the output file is also
included.

E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.

EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX, and inhomogeneous clusters of UNIX workstations under PVM or MPI. EGO also runs sequentially on any decent UNIX workstation, even Windows95/NT PC's (with a GNU-C compiler) can be used.

Genpak is a small set of utilities designated to process DNA, RNA, and protein sequences in a very Un*x-like manner. This way, Genpak programs can be combined using pipes and redirections, as well as easily incorporated into CGI scripts. The utilities include a program for calculating GC content, Tm, translating DNA/RNA sequences into protein sequences, quick sequence retrieval, random sequence generation, and finding promoter sequences using a Hertz matrix.

Ghemical is a molecular modelling software package with some nice 3D visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). The geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms are included. Ghemical is written in C++, and hopefully offers a good framework for a generic freeware molecular modelling tool.